Florian Mueller, a German software savant, is invaluable to many in the public and media for his ability to explain the arcane patent battles engulfing companies like Google (NSDQ: GOOG) and Apple (NSDQ: AAPL). But is Mueller’s keen analysis being swayed by his ties to Microsoft?

On his popular FOSS Patents blog, Mueller summarizes in plain English the legal wrangling surrounding disputes like Apple’s effort to snuff out Samsung. A self-styled intellectual-property expert, his quick quotes have made him popular with blogs and major news outlets alike.

On Friday, the 9To5 Google blog pointed to a post in which a Google software engineer noted that Mueller had disclosed that he received money from Microsoft (NSDQ: MSFT) for a new study. The engineer also described Mueller as “anti-Google” and pointed out that he is a patent analyst not a lawyer.

So what should we make of Mr. Mueller? The engineer’s assessment is fair in one sense but unfair in another. Let’s start with the latter. As a former practicing lawyer, I don’t believe one needs a law degree to understand or report on law. In Mueller’s case, he is able to parse and summarize tricky judgments more effectively than many of his credentialed counterparts and does not make any obvious mistakes. He is very smart and his blog provides an excellent way to keep up with the tic-toc of global software patent litigation. As for the Microsoft-funded study, it seems a worthy enough initiative (a review of FRAND patents) and Mueller has the qualifications to undertake it.

The problem lies not with Mueller’s analysis — but with his impartiality. The engineer is right when he says that Mueller has the knives out for Google. Even a casual reader of the FOSS blog can easily discern that Mueller is quick to amplify any legal setback for Google’s Android or its affiliates. His tone can be crowing and haughty — see the tendentious “Google scores an Own Goal” post about Motorola (NYSE: MMI) — and for all the world echoes Microsoft’s own “they’re getting what they deserve” attitude to Google.

In a friendly email, Mueller said he calls things as he sees them and that he is typically validated by what happens in court. He gave examples (some of which were overstated — like Google’s failure to win a summary judgment motion). But he did not address the larger question of whether he is selective in what he does and does not report.

“I don’t see a conflict of interest between my work as an analyst and my blogging activity,” he wrote. “I have had consistent positions for many years. For example, my position on the immense strength of Microsoft’s patent portfolio has always been the same whether I worked with them or against them. During my campaign against software patents on Europe I repeatedly warned the industry and the public at large against the strategic leverage that Microsoft and other large players — but especially Microsoft — had and would have in the future thanks to their patent holdings.”

He says that he and Microsoft have worked together more than once, but that because of a confidentiality agreement with the company, he can’t elaborate on the details of that relationship. “I have a large number of clients, and there will always be some I cannot disclose due to confidentiality obligations.” On his web site, he says that his “consulting services are available directly as well as through three primary research firms (Gerson Lehrman Group, Coleman Research Group, Guidepoint Global Advisors) serving the financial community.”

The relationship between Mueller and Microsoft is noteworthy for another reason: Microsoft’s history of using proxies to attack Google. Prior to hearings on the Google Books Settlement, for instance, Microsoft paid a professor and former employee to run a project summarizing objections to the settlement.And the Wall Street Journal (NSDQ: NWS) reported that Microsoft lawyers were behind the efforts of an obscure Ohio company to bring an antitrust action against Google.

Mueller may have perfectly good reasons to consistently zing Android — he’s far from the only pundit that has consistently strong views about a particular company. But given his financial relationship with that company’s archenemy– and the fact that Microsoft has a history of “hiring” outside experts to attack the competition — it’s hard to regard him as a disinterested party. The time has come for Mueller to amend the conflict of interest disclaimer on his blog and for the media to cease citing him as an impartial authority.